It happens often. You cut to the best performance of a character, and another character steps on the line. Picture departments often will find an alternate reading to "clean up" the area were the overlap of lines happen. However, it is still important that sound editorial has access to the original line reading.
So what you do in these situations is keep the original production in one of your tracks, but bring it down to zero (infinity on the audio mix tool). That way, you get your clean line reading for screenings, but sound has access to the sync track when you turn over your OMFs.
This is a very simple thing to do and will save time down the road.